Open up iFile and got to //var/stash
You'll see a bunch of folders with names ending in .******
tap the blue arrow next to Themes.****** to bring up the File Attributes screen
turn on Apply hierarchically and tap done

This will apply the folder's permissions and ownership properties to all the files and folders inside that folder, so all of your themes (and the files inside them) will have the suitable permissions.

Now open Winterboard > Select Themes > and disable, then enable the theme folder that contains the wonky icon.
tap the Winterboard back button and tap Respring to re-apply the theme.

If you're certain the folder and file are named correctly the icon should be themed for sure now.